Committed in r3784. Note that this is really a bugfix rather than a patch, so I've left out the option to avoid it. Also, I made a slight modification to your code to take account of the 'order' variable.
- Noel On 10 June 2010 14:47, Richard Hall <r.h...@astex-therapeutics.com> wrote: > Hi Noel, > > ( I've cc'ed this message to the openbabel-devel list as suggested, so you > have a record of the patch :) ) > > The use of multiple conect records to define bond orders is not a part of the > pdb standard, but there does appear to be limited support for this in the pdb > parser currently - if the same connection appears multiple times *on the same > line* then the bond order is derived from this. If the same connection > appears over separate lines then only the information on the first line is > used. Consider the Y3 ligand from the pdb file 1a5v - I've attached an > 'astex mode' ligand pdb file, where the connections to eg sulfur 1144 span > two lines > > CONECT 1144 1134 1145 1145 1146 > CONECT 1144 1146 1147 > > The S=O bond, 1144-1146 is split across two lines. Using the current > openbabel pdbformat parser, the output smiles string is > > c1(cc(cc2c1c(cc(c2)[S](=O)(O)O)NC(=O)C)[S](=O)(O)O)O > > if you switch to using my patched pdbformat parser (diff file attached - note > this is a diff from the v2.3.3 source code), you end up getting > > c1(cc(cc2c1c(cc(c2)S(=O)(=O)O)NC(=O)C)S(=O)(=O)O)O > > which is 'more correct' in this instance. My patch has 'astex mode' turned > on by default, but you can revert to the original algorithm by adding the -aa > flag. Note that I haven't tested this to destruction, but it seems to be > doing a good job for ~4000 test pdb ligands containing astex style conect > records. > > Thanks also for the pybel advice - with 'astex mode' as the default I don't > need the switch currently, but I will have a look at that OBConversion object > as I am bound to need it at some point. > > cheers - enjoy the summer, the holidays and your conferencing! > Richard > > -----Original Message----- > From: Noel O'Boyle [mailto:baoille...@gmail.com] > Sent: 10 June 2010 11:16 > To: Richard Hall > Subject: Re: pybel and openbabel > > On 10 June 2010 09:57, Richard Hall <r.h...@astex-therapeutics.com> wrote: > > Hi Richard, > > How's the goin'? > >> hope all is well with you > > It is indeed. > >> - I have recently been using PyBel for a >> cheminformatics project and have hacked the OpenBabel pdb file reader >> slightly to cope with the 'Astex way' of dealing with conect records (*). I >> was wondering whether I should submit a patch for this? Rather than trample >> the default behaviour, my change requires a switch when running OpenBabel >> (-aa) > > Great. Patches always very welcome, especially for the PDB parser > (which I may one day actually get around to using). Seeing as this > isn't the first Astex contribution, do you want commit access? > Otherwise, I can sort it out myself if you send me a patch (also a > good idea to cc to openbabel-de...@lists.sf.net if you're happy with > this - means we have a record of the patch). > > One thing I don't understand is whether you are talking about reading > custom PDB files or PDB files actually from the PDB, because it would > be strange if their own PDB files didn't conform to their standard. > >> - how much work would it be to get the Pybel readfile method to >> include these switches? > > Someone just asked me about this also so it's on my mind. The reason > I'm reluctant is because I feel this is moving into 'advanced usage' > territory, but I'll think about it. In the meanwhile, you need to use > the underlying OBConversion object yourself as shown at > http://baoilleach.blogspot.com/2008/10/generating-inchis-mini-me-inchikey.html. > >> I hope that makes sense? Are you going to the Sheffield conference? If so >> I'll see you there! > > I'm all conferenced out for this year, except for Goslar in November. > I was planning to go to PyCon this time round, but it clashes with > holidays. > > - Noel > >> best wishes >> >> Richard >> >> >> >> (*) We use the number of occurrences of a connect record to determine bond >> order and these occurrences can span multiple lines - I was finding that the >> sulfur in a CS(=O)(=O)C motif would have connect records running over two >> lines and the current way of doing things does not cope with this - I would >> end up with a smiles that looked like C[S@@](=O)(O) >> >> >> >> Disclaimer >> >> This communication is confidential and may contain privileged information >> intended solely for the named addressee(s). It may not be used or disclosed >> except for the purpose for which it has been sent. If you are not the >> intended recipient you must not review, use, disclose, copy, distribute or >> take any action in reliance upon it. 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